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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        About MultiQC

        This report was generated using MultiQC, version 1.31

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-09-29, 21:23 MDT based on data in: /home/moji-lin/rna-seq-reanalysis/data/processed

        General Statistics

        Showing 18/18 rows and 11/17 columns.
        Sample NameError rateNon-primaryReads mapped% Mapped% Proper pairs% MapQ 0 readsTotal seqsMean insertReadsReads mapped% Reads mapped% AlignedM AlignedLibrary typesCFRM Bias% Aligned
        processed | Bam_related_logs | logs_trimmed_KO_SRR13633857 | trimmed_KO_SRR13633857
        0.15%
        5.6M
        26.8M
        98.3%
        0.0%
        0.3%
        27.3M
        0.0bp
        32.9M
        32.4M
        98.6%
        98.3%
        processed | Bam_related_logs | logs_trimmed_KO_SRR13633858 | trimmed_KO_SRR13633858
        0.15%
        5.6M
        26.7M
        98.1%
        0.0%
        0.4%
        27.2M
        0.0bp
        32.9M
        32.4M
        98.4%
        98.1%
        processed | Bam_related_logs | logs_trimmed_KO_SRR13633859 | trimmed_KO_SRR13633859
        0.15%
        5.5M
        27.0M
        98.4%
        0.0%
        0.4%
        27.4M
        0.0bp
        32.9M
        32.4M
        98.7%
        98.4%
        processed | Bam_related_logs | logs_trimmed_KO_SRR13633860 | trimmed_KO_SRR13633860
        0.15%
        5.4M
        26.9M
        98.4%
        0.0%
        0.4%
        27.4M
        0.0bp
        32.8M
        32.4M
        98.7%
        98.4%
        processed | Bam_related_logs | logs_trimmed_WT_SRR13633855 | trimmed_WT_SRR13633855
        0.14%
        6.2M
        27.0M
        98.5%
        0.0%
        0.4%
        27.4M
        0.0bp
        33.6M
        33.2M
        98.7%
        98.5%
        processed | Bam_related_logs | logs_trimmed_WT_SRR13633856 | trimmed_WT_SRR13633856
        0.15%
        6.7M
        27.0M
        98.4%
        0.0%
        0.4%
        27.4M
        0.0bp
        34.1M
        33.7M
        98.7%
        98.4%
        processed | quant_results | trimmed_KO_SRR13633857 | trimmed_KO_SRR13633857
        100.0%
        0.5
        processed | quant_results | trimmed_KO_SRR13633858 | trimmed_KO_SRR13633858
        100.0%
        0.5
        processed | quant_results | trimmed_KO_SRR13633859 | trimmed_KO_SRR13633859
        100.0%
        0.5
        processed | quant_results | trimmed_KO_SRR13633860 | trimmed_KO_SRR13633860
        100.0%
        0.5
        processed | quant_results | trimmed_WT_SRR13633855 | trimmed_WT_SRR13633855
        100.0%
        0.5
        processed | quant_results | trimmed_WT_SRR13633856 | trimmed_WT_SRR13633856
        100.0%
        0.5
        quant_results | trimmed_KO_SRR13633857 | aux_info | trimmed_KO_SRR13633857
        94.5%
        25.8M
        U
        quant_results | trimmed_KO_SRR13633858 | aux_info | trimmed_KO_SRR13633858
        93.8%
        25.6M
        U
        quant_results | trimmed_KO_SRR13633859 | aux_info | trimmed_KO_SRR13633859
        94.3%
        25.8M
        U
        quant_results | trimmed_KO_SRR13633860 | aux_info | trimmed_KO_SRR13633860
        93.9%
        25.7M
        U
        quant_results | trimmed_WT_SRR13633855 | aux_info | trimmed_WT_SRR13633855
        94.5%
        25.9M
        U
        quant_results | trimmed_WT_SRR13633856 | aux_info | trimmed_WT_SRR13633856
        93.0%
        25.5M
        U

        Samtools

        Version: 1.19.2 HTSlib: 1.19

        Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

        Percent mapped

        Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

        For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

        Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

        Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

        Created with MultiQC

        Alignment stats

        This module parses the output from samtools stats. All numbers in millions.

        Created with MultiQC

        Flagstat

        This module parses the output from samtools flagstat

        Created with MultiQC

        Flagstat: Percentage of total

        This module parses the output from samtools flagstat

        Created with MultiQC

        Salmon

        Version: 1.10.3

        Quantifies expression of transcripts using RNA-seq data.URL: https://combine-lab.github.io/salmonDOI: 10.1038/nmeth.4197

        Created with MultiQC

        Bowtie 2 / HiSAT2

        Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4

        Single-end alignments

        This plot shows the number of reads aligning to the reference in different ways.

        There are 3 possible types of alignment:

        • SE mapped uniquely: Read has only one occurence in the reference genome.
        • SE multimapped: Read has multiple occurence.
        • SE not aligned: Read has no occurence.
        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        SalmonSalmon1.10.3
        SamtoolsHTSlib1.19
        Samtools1.19.2